siRNA Compositions and Methods for Treatment of HPV and Other Infections

ABSTRACT

The invention provides siRNA compositions that (1) interfere with viral replication of human papillomavirus (HPV), herpes simplex virus (HSV), and human immunodeficiency virus (HIV) in mucosal tissues, such as genital tissues, and (2) treat fungal infections. The compositions include siRNA molecules that target HPV, complexed with a dendrimer that treats and prevents genital herpes (HSV) and HIV. The compositions also include siRNA molecules that target HPV, complexed with a histidine-lysine (HK) polymer that treats and prevent fungus infection. The combined formulations of siRNA and dendrimer provide treatment of the infections from HPVs, HSVs, and HIVs. The combined formulations of siRNA and HK polymer provide treatment of HPVs and fungus infections.

CROSS-REFERENCE TO RELATED PATENT APPLICATIONS

This application is a continuation-in-part of, and claims the benefit under 35 U.S.C. §§120 and 365(c) of, International Patent Application No. PCT/US2011/045884, filed Jul. 29, 2011, which claims priority to, and the benefit of, U.S. Provisional Patent Application No. 61/369,067, filed Jul. 29, 2010, the contents of each of which are expressly incorporated by reference herein in their entirety.

FIELD OF INVENTION

The invention relates to siRNA molecules, compositions, and methods for the treatment of human papillomavirus (HPV) infections and certain other infections, in particular, HIV, HSV, and fungal infections. The compositions include a cocktail of siRNA molecules targeted against HPV, formulated with dendrimer, a polymer which is effective against HIV and HSV infections. The compositions also include a cocktail of siRNA molecules targeted against HPV, formulated with histidine-lysine (HK) polymer, a polymer which has been shown to be effective in vitro to inhibit fungal infections.

BACKGROUND HPV and Cervical Cancer

Human Papilloma Virus (HPV) is a group of coated DNA viruses, which now has over 100 different species, and is the most common sexually transmitted (ST) infection in adults worldwide. In 1976 Harald zur Hausen from Germany published the hypothesis that human Papilloma virus plays an important role in the cause of cervical cancer tissue[1]. In 1983 and 1984 zur Hausen and his collaborators identified HPV16 and HPV18 in cervical cancer [2-4]. Dr. zur Hausen was awarded the Nobel Prize for Physiology and Medicine in 2008, because of his contribution. It is estimated that over 80% of US women by age 50 will have contracted at least one strain of HPV[5]. It is also estimated that each year there are 490,000 new cases of cervical cancer worldwide, which result in 270,000 deaths. In the US, each year there are 250,000 to 1 million women who develop cervical dysplasia, which leads to 11,000 further developing cervical cancer, and to 4,000 deaths [6]. Among the 19 “high-risk” HPVs which will lead to cervical cancer, HPV16 and 18 count for about 70% of the cases[7].

HPVs have a circular genome of about 8 kb, with three major regions in the genome, the early genes (E6, E7, E1, E2, E4 and E5), the late genes (L1 and L2), and the long control region (LCR) between L1 and E6. FIG. 1 shows the characteristic HPV genome organization, using the medically important HPV-18 as the model. The early transcripts ending at 4215 encode the 6 early genes, while the late transcripts ending at 7221 encode the two late genes. E6 and E7 are cancer transforming proteins because they inactivate tumor suppressor proteins p53 (inactivated by E6) and pRb (inactivated by E7) [8].

Although the US FDA has approved two HPV vaccines (below), there is still a high demand for HPV therapeutics. However, there is no effective treatment on the market yet [9]. This invention describes HPV therapeutics by siRNAs complexed with dendrimer and histidine-lysine polymers.

HPV Vaccine

In 2006, the US FDA approved Gardasil®, an HPV vaccine produced by Merck, which is composed of hollow virus-like particles (VLP) assembled from recombinant HPV coat proteins and which targets HPV 16, 18, 6 and 11. The vaccine is aimed at use in women and girls. Later, it was reported that Gardasil® is also effective in preventing genital warts in males. The use of Gardasil® for men and boys was approved by the FDA on Oct. 16, 2009. In October 2009, the FDA also approved Cervarix®, the second HPV vaccine targeting HPV16 and 18 and produced by GlaxoSmithKline [10].

Public health officials in industrialized counties and areas like Australia, Canada, Europe and the US recommend vaccination of young women against HPV to prevent cervical cancer and genital warts, and to reduce the number of painful and costly treatments for cervical dysplasia caused by HPV infections. It is recommended that women and girls who are not exposed to HPVs between the ages of 9 to 25 should get an HPV vaccination [11]. However, many women and girls are not vaccinated because of various reasons. In the US, only about one-quarter of girls got HPV vaccination because most families worried about either the effectiveness or the side effects of the vaccine [12]. In addition, HPV vaccines are not very easy to get access to in third world countries. In Kenya as an example, the cost of vaccination is over the average annual income of a family [13]. Furthermore, many women have been exposed to HPVs already [14].

Dendrimer and Clinical Trials for HIV and HSV Treatment and HPV Inhibition In Vitro

Dendrimers are dendritic polymers which belong to a new class of polymer architecture (after traditional linear, cross-linked and branched types)[15]. VivaGel® (SPL7013), an anionic poly (L-Lysine) dendrimer, has been applied in at least 4 different clinical trials [16]. A phase I trial, completed on Jan. 20, 2008, tested male tolerance for topical application of SPL7013. Phase I and II trials, completed on Jun. 4, 2009, of vaginal dosing tested against HIV infection and HSV-2 herpes in women. A phase I trial, completed on Feb. 2, 2010, tested acceptability of SPL7013 in sexually active women. A phase I trial, completed on Mar. 4, 2010, was a safety test for HSV-2 infection in health young women. Australian and US NCI laboratories also showed that SPL7013 inhibits clinically relevant strains of HPV in vitro [17].

HK Polymers Inhibit Fungal Infections In Vitro

It was shown that histidine-lysine polymers are able to inhibit the growth of fungal strains, C. albicans and C. kefyr [18]. The highest inhibition activity was achieved by HK polymer H2K4b (MW, 11,137). The structure of H2K4b is as follows: KKK(KHKHHKHHKHHKHHKHHKHK)4

RNAi and Development of Novel Therapeutics

RNA interference (RNAi) was first illustrated in plants, but quickly proved to be a universal process covering low and high biological species. It is an efficient process in which double-stranded RNA duplexes were generated and lead to sequence specific target RNA recognition, binding and degradation[19]. In recent years RNAi was not only applied in various biological studies, but applied in therapeutic development as well [20]. To date, at least 15 therapeutic programs developed from RNAi are in different stages of or have finished clinical trials [21].

Delivery Vehicles for siRNA Therapeutics

Even though siRNAs provide a very attractive technology to be developed into innovative therapeutics, many of the programs didn't succeed. Failed siRNA therapeutic programs either in preclinical studies or in clinical trials have proved that siRNA molecules designed to target various genes could not apply to animals or human beings directly because of stability issues [20]. Naked siRNAs have to be modified to protect them from degradation, or to be packed with other molecules either to facilitate cell entry or to be functional to decrease target gene expression [22]. Therefore, the development of delivery methods has been one of the most important areas in the research and development of siRNA therapeutics [23].

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A. HPV Genome and siRNA Designed Targeting Hybrid E7 Gene from HPV16 and Cotton Rabbit Papilloma Virus (CRPV). The E7 gene is enlarged in the bottom and with the three CRPV motifs marked as red blocks.

FIG. 1B. SiRNA Designed Targeting Wild-type E7 gene of HPV16 and Hybrid E7 Gene from HPV16 and CRPV. The red blocks are CRPV sequences used to replace the correspondent HPV16 fragments. The yellow highlights in the CRPV E7 siRNAs reflect the codon optimization results.

FIG. 1C. Chimeric human rabbit papilloma virus (cH-RPV) gene construction. The 3 epitope sequences A, B and C (corresponding to the red blocks highlighted in FIGS. 1A and 1B) from HPV16 E7 gene were inserted in the end of CRPV E7 gene in the same reading frame.

FIG. 2. psiCHECK-1 map.

FIG. 3. Rabbit Skin Model of Papilloma Virus Infection.

FIG. 4A. 25 mer siRNA is more potent than 21 mer siRNA.

FIG. 4B. 25 mer siRNA is more potent than 21 mer siRNA.

FIG. 5. HPV16 E7 Expression Knocking Down by siRNAs in SiHa Cells.

FIG. 6. HPV16 E7 Expression Knocking Down by CRPV Hybrid siRNAs in SiHa Cells.

FIG. 7. The effect of the first batch siRNAs on knocking-down of HPV18E7 mRNA expression.

FIG. 8. The potent siRNAs are capable of reducing the E7 gene expression in the SiHa cell line. Four siRNAs against the hybrid E7 gene were further tested for their ability to reduce the E7 protein expression in SiHa cells. The Western blot (top) and quantitative data (bottom) showed that the potency of the siRNA reducing the E7 protein expression are listed in this order, —45>−43>−44>−37, which fit the results in the qRT-PCR experiment.

FIG. 9. Rabbit skin inoculated with different papilloma virus, and treated with different siRNA-HKP paste (L). Elizabethan collars were applied to the animals to prevent disturbance of the treated area by the animal (R).

FIG. 10. SiRNA (siNA-CRPV-43) treatment inhibited the skin warts growth induced by cH-RPV in the rabbit model (L), data (R).

FIG. 11. Data summary of the treatment of cH-RPV by different siRNAs. The effective siRNAs are highlighted.

DESCRIPTION OF THE INVENTION

The invention provides siRNA molecules, compositions containing the molecules, and methods for using the molecules and compositions to treat HPV infections and certain other infections, in particular, HIV, HSV, and fungal infections. The compositions include a cocktail of siRNA molecules targeted against HPV, formulated with dendrimer, a polymer which is effective against HIV and HSV infections. The compositions also include a cocktail of siRNA molecules targeted against HPV, formulated with histidine-lysine (HK) polymer, a polymer which has been shown to be effective in vitro to inhibit fungal infections.

As used herein, an “siRNA molecule” or an “siRNA duplex” is a short, double-stranded oligonucleotide that interferes with the activity of RNA expressed by a gene in a cell, after the molecule is introduced into the cell. The molecules are constructed by techniques known to those skilled in the art, given the teachings disclosed herein. Such techniques are described in U.S. Pat. Nos. 5,898,031, 6,107,094, 6,506,559, and 7,056,704 and in European Pat. Nos. 1214945 and 1230375, which are incorporated herein by reference in their entireties.

The siRNA molecule of the invention is an isolated siRNA molecule that binds to a single stranded RNA molecule, which is a messenger RNA (mRNA) that encodes at least part of a peptide or protein of a human papillomavirus (HPV). The mRNA can be encoded by any gene in an HPV, including an early or late stage viral proliferation gene. In one embodiment, the siRNA molecule binds to mRNA molecules from different species of HPV. In one particular embodiment, the HPV species is HPV 16, HPV 18, HPV6, or HPV 11.

In one embodiment, the molecule is an oligonucleotide with a length of about 19 to about 35 base pairs. In another embodiment, the molecule is an oligonucleotide with a length of about 19 to about 27 base pairs. In still another embodiment, the molecule is an oligonucleotide with a length of about 21 to about 25 base pairs. In one particular embodiment, it has 25 base pairs. In all of these embodiments, the molecule may have blunt ends at both ends, or sticky ends at both ends, or a blunt end at one end and a sticky end at the other. In one particular embodiment, it has blunt ends at both ends.

The siRNA molecule can be made of naturally occurring ribonucleotides, i.e., those found in living cells, or one or more of its nucleotides can be chemically modified by techniques known in the art. In addition to being modified at the level of one or more of its individual nucleotides, the backbone of the oligonucleotide also can be modified. Additional modifications include the use of small molecules (e.g. sugar molecules), amino acid molecules, peptides, cholesterol and other large molecules for conjugation onto the siRNA molecules. Such modifications can protect the molecule from degradation, improve its potency, reduce its toxicity, and reduce its immune stimulatory effect.

The siRNA molecule may further comprise an immune stimulatory motif. Such motifs can include specific RNA sequences such as 5′-UGUGU-3′ (Judge et al., Nature Biotechnology 23, 457-462 (1 Apr. 2005)), 5′-GUCCUUCAA-3′ (Hornung et al., Nat. Med. 11, 263-270 (2005). See Kim et al., Mol Cell 24; 247-254 (2007). These articles are incorporated herein by reference in their entireties. These are siRNA sequences that specifically activate immune responses through Toll-like receptor (TLR) activation or through activation of key genes such as RIG-I or PKR. In one embodiment, the motif induces a TH1 pathway immune response. In another embodiment, the motif comprises 5′-UGUGU-3′,5′-GUCCUUCAA-3′,5′-GGGxGG-3′ (where x is A, T, G and C), or CpG motifs 5′-GTCGTT-3′.

Particular target sequences are shown in Tables 1-4 herein. Thus, certain particular siRNA molecules of the invention bind to and inhibit expression of one or more of the sequences identified in these tables. Because the siRNA molecules are duplexes, with one strand being complementary to the target mRNA and the other including the same sequence as the target sequence in the mRNA, the sequences shown in Tables 1-4 also represent certain specific siRNA molecules of the invention.

The siRNA molecules of the invention also include ones derived from those listed in Tables 1-4. The derived molecules can have less than the 25 base pairs shown for each duplex, down to 16 base pairs, so long as the “core” base pairs remain. That is, once given the specific sequences shown in the tables, a person skilled in the art can synthesize molecules that, in effect, “remove” one or more base pairs from either or both ends in any order, leaving the remaining contiguous base pairs, creating shorter molecules that are 24, 23, 22, 21, 20, 19, 18, 17, or 16 base pairs in length. Thus, the derived molecules consist of: a) 24 contiguous base pairs of any one or more of the molecules in Tables 1-4; b) 23 contiguous base pairs of any one or more of the molecules in Tables 1-4; c) 22 contiguous base pairs of any one or more of the molecules in Tables 1-4; b) 21 contiguous base pairs of any one or more of the molecules in Tables 1-4; d) 20 contiguous base pairs of any one or more of the molecules in Tables 1-4; e) 19 contiguous base pairs of any one or more of the molecules in Tables 1-4; f) 18 contiguous base pairs of any one or more of the molecules in Tables 1-4; g) 17 contiguous base pairs of any one or more of the molecules in Tables 1-4; and h) 16 contiguous base pairs of any one or more of the molecules in Tables 1-4. It is not expected that molecules shorter than 16 base pairs would have sufficient activity or sufficiently low off-target effects to be pharmaceutically useful; however, if any such constructs did, they would be equivalents within the scope of this invention.

Alternatively, the derived molecules can have more than the 25 base pairs shown for each duplex, so long as the “core” base pairs remain. That is, once given the specific sequences shown in the tables, a person skilled in the art can synthesize molecules that, in effect, “add” one or more base pairs to either or both ends in any order, creating molecules that are 26 or more base pairs in length and containing the original 25 contiguous base pairs.

In one embodiment, the molecule includes a potency enhancer motif. As used herein, a potency enhancer motif (PEM) is a sequence in the siRNA molecule that increases the therapeutic effect of the molecule in an animal model compared to the same molecule without the sequence. Examples of such motifs are ACTCC and GGAGT.

The invention also includes compositions of one or more of the siRNA molecules. Where there is a plurality of different siRNA molecules, each one targets a different RNA nucleotide sequence, which can be on the same RNA target molecule, different RNA target molecules, or any combination thereof. These compositions, by themselves or in combination with pharmaceutically acceptable carriers such as those described herein, are sometimes called siRNA cocktails. Thus, the invention provides multi-targeted siRNA cocktails for the treatment of HPV.

All possible combinations of types of molecules and targets are included in the invention. For example, the targeted mRNA molecules may encode or regulate the expression of one or more HPV proteins. In one embodiment, the composition comprises two or more different siRNA molecules, each binding to a different mRNA target sequence. In another embodiment, the composition comprises three different siRNA molecules, each binding to a different mRNA target sequence. In still another embodiment, the composition comprises more than three different siRNA molecules, each binding to a different RNA target sequence. In one embodiment, the siRNA molecules target one or more of the mRNA sequences that are transcribed from one or more of the gene sequences listed in Tables 1-4 herein. For example, the cocktail can inhibit expression of one or more of HPV E6, E7, E1, E2, E4, E5, L2, and L1 genes in human tissue. In one embodiment, it inhibits expression of two or more HPV E6, E7, E1, E2, E4, E5, L2, and L1 genes.

As previously mentioned, the siRNA cocktails of the invention comprise two or more different siRNA molecules of the invention in a pharmaceutically acceptable carrier. Such carriers are generally known to those skilled in the art and include saline, sugar solutions, polypeptides, polymers, lipids, creams, gels, micelle materials, and metal nanoparticles.

In one embodiment, the carrier comprises at least one of the following: a glucose solution, a polycationic binding agent, a cationic lipid, a cationic micelle, a cationic polypeptide, a hydrophilic polymer grafted polymer, a non-natural cationic polymer, a cationic polyacetal, a hydrophilic polymer grafted polyacetal, a ligand functionalized cationic polymer, a ligand functionalized-hydrophilic polymer grafted polymer, a ligand functionalized liposome, dendrimer, dendrimer solutions, HK polymer, and HK polymer solutions. Examples of polymers include a biodegradable histidine-lysine polymer, a biodegradable polyester, such as poly(lactic acid) (PLA), poly(glycolic acid) (PGA), and poly(lactic-co-glycolic acid) (PLGA), a polyamidoamine (PAMAM) dendrimer, a cationic lipid, or a PEGylated PEI. Cationic lipids include DOTAP, DOPE, DC-Chol/DOPE, DOTMA, and DOTMA/DOPE. In still another embodiment, the carrier is a histidine-lysine copolymer that forms a nanoparticle with the siRNA molecule, wherein the diameter of the nanoparticle is about 100 nm to about 400 nm.

The invention also provides a nanoparticle comprising one or more of the siRNA molecules of the invention, a pharmaceutically acceptable carrier, such as one or more of those described herein, and a targeting ligand. Examples of such ligands include one or more of an RGD peptide, such as H-ACRGDMFGCA-OH, an RVG peptide, such as H-YTIWMPENPRPGTPCDIFTNSRGKRASNG-OH, or a FROP peptide, such as H-EDYELMDLLAYL-OH.

The molecules and compositions of the invention interfere with viral replication of HPV. Certain of the compositions also (1) interfere with viral replication of herpes simplex virus (HSV) and human immunodeficiency virus (HIV) in mucosal tissues, such as genital tissues, and (2) treat fungal infections. The molecules and compositions of the invention are used to treat and/or prevent HPV, HSV, HIV, and fungal infections.

The invention also provides a method of treating a mammal with an HPV infection by administering to the mammal a therapeutically effective amount of one or more of the siRNA molecules of the invention or a therapeutically effective amount of one or more of the compositions of the invention. In one embodiment, the mammal is a human, non-human primate, or rodent, such as a mouse, rat, or guinea pig. Rodents are particularly useful for laboratory experiments. In a particular embodiment, the mammal is a human patient.

The compositions are administered by techniques known to those skilled in the art. In one embodiment, the composition comprises at least three siRNA molecules at a ratio determined by the potency of each siRNA molecule and the therapeutic needs of the mammal. In another embodiment, the composition comprises three different siRNA molecules at a ratio of 1:1:1, 1:1.5:0.5, or 0.5:0.5:2.

Certain compositions of the invention have an anti-HIV and an anti-HSV activity, and others have an anti-fungal activity. As mentioned above, dendrimer has an anti-HIV and an anti-HSV activity, and HK polymer has an anti-fungal activity. Therefore, the invention includes a method of treating a mammal with an HPV infection and with an HIV and/or HSV infection comprising administering to the mammal a pharmaceutically effective amount of a composition comprising one or more siRNA molecules of the invention and dendrimer. It further includes a method of treating a mammal with an HPV infection and a fungal infection comprising administering to the mammal a pharmaceutically effective amount of a composition comprising one or more siRNA molecules of the invention and an HK polymer.

The compositions of the invention also can be used with a therapeutically effective amount of other anti-infective agents.

The siRNA molecules and compositions of the invention can also be used prophylactically against HPV, HSV, HIV, and fungal infections. A therapeutically effective amount of one or more of the siRNA molecules of the invention or a therapeutically effective amount of one or more of the compositions of the invention are administered to a mammal. In one embodiment, the mammal is a human patient.

The following examples illustrate certain aspects of the invention and should not be construed as limiting the scope thereof.

EXPERIMENTAL DESIGN, TECHNIQUES, AND EXAMPLES

Prepare Potent siRNA Duplexes Targeted to Genes in HPV16, HPV18, HPV6, and HPV 11

In the preliminary studies, we have demonstrated that 25-mer siRNAs are most potent at inhibiting the expression of a specific gene. To ensure the potency of each siRNA molecule for the target gene knockdown, several key features should be considered during the in silico design and the later in vitro and in vivo tests so that the siRNAs:

(1) have the optimum thermodynamics for target sequence binding; (2) have sufficient length for RISC binding; (3) have eliminated (or added) immune stimulating motifs; (4) have minimized “Off-Target” potential; (5) pass through patent searching with no conflict with the current patents; and (6) have no interaction when multiple sequences are mixed in a cocktail.

In this invention, we designed siRNA duplexes targeting the conserved gene sequences shared by as many HPV species as possible to increase the universality of the siRNAs. In addition, our preliminary results have demonstrated that 25mer siRNA is more potent than 21mer siRNA. We use 25mer siRNA as our design for the multi-targeted siRNA cocktail targeting to both early (E6, E7, E1, E2, E4, E5) and late (L2 and L1) genes simultaneously (FIG. 1A). All the gene silencing potencies were tested and validated first in the cell culture experiments by RT-PCR and ELISA for efficacy of multi-targeting siRNA on gene knockdown at both transcription and translation levels. Once the most effective siRNA duplexes are selected for both early and late genes from the gene knockdown experiments in cell culture models, we further investigated the optimal combination of siRNA set as the active pharmaceutical ingredient (API) and tested optimized siRNA combinations in a rabbit model.

Applying our siRNA duplexes in cell based high throughput screening, we were able to select the most effective siRNA molecules to reduce HPV16, HPV18, HPV6, and HPV 11 gene expression. The siRNAs target all 8 genes of E6, E7, E1, E2, E4, E5, L2 and L1 from HPV16, 18, 6 and 11 with some of the siRNA incorporating the Potency Enhancer Motif (PEM) sequence. (See below.)

Molecular Design of siRNA Sequence

Table 1 shows the siRNAs designed against the 7 genes from HPV16 (with no qualified siRNAs for the E5 gene). Table 2 shows the siRNAs designed against the 8 genes in HPV18. Tables 3 and 4 are the common siRNAs for both HPV6 and HPV11. Generally, we choose 8 siRNAs for each gene. If there are not enough qualified siRNAs, the number will be less than 8. The genes are arranged according to the transcription starting sites. Each gene also marked the transcription start and stop sites. The Potency Enhancer Motif (PEM) sequence (GGAGT) and the reversed strand (ACTCC) are highlighted with yellow or green, respectively.

We have designed 8 siRNAs for each gene in HPV strain (selected from about 400 siRNA pools for each HPV strain). The following are the specific sequences of siRNA targeting each gene for each individual HPV strain. In HPV16, we did not find any qualified siRNA for gene E5 based on the parameters we set for selection in silico in above section. In addition, we found only 7 qualified siRNAs for gene E4. Furthermore, #163 and #167 target both genes of E2 and E4. The overlap has reduced the total number of unique sequences of siRNA for HPV16 to 53 (Table 1).

In HPV18, there are only 7 and 6 siRNA molecules which are qualified for gene E4 and E5, respectively, based on our selection criteria summarized in previous section (Table 2). In addition, #173 and #178 target both genes E2 and E4. Thus, our total number of unique siRNAs for HPV18 is reduced to 59 (Table 2).

In contrast with HPV16 and 18, where we could not find any siRNAs of 25-mer which share the same the common sequence between 16 and 18, in HPV6 and 11, among the siRNAs we have designed (about 250 for each), we have found 10 common siRNAs for both HPV-6 and HPV-11 as shown in Table 3. The 10 common siRNAs target the following genes in both HPV6 and 11: E7, E1, E2, L2 and L1. The common siRNAs found in HPV6 and 11 has made our selection process simpler and easier. We only need to synthesize the 10 siRNAs and test their ability to reduce the expression of HPV6 and 11 genes.

In order to screen potent siRNAs in an in vivo rabbit model [24], we have inserted a codon optimized cotton rabbit papilloma viral (CRPV) gene motif in HPV16 E7, and designed siRNAs to target the CRPV motif and adjacent HPV16 E7 gene (FIGS. 1A and 1B, Table 4). The siRNAs were screened in SiHa cells to choose the ones which can knock down the E7 gene expression.

Potency Enhancer Motif (PEM) Sequence

Table 1 lists the siRNAs designed against the 8 genes from HPV16. Table 2 lists the siRNAs designed against the 8 genes in HPV 18. Table 3 and 4 are the common siRNA molecules targeting both HPV6 and HPV11. The genes are arranged according to the transcription starting sites. Each gene also marked the transcription start and stop sites. The Potency Enhancer Motif (PEM) sequence (GGAGT) and reversed strand (ACTCC) are shown.

We chose 8 siRNAs molecules for each of the 8 genes in both HPV16 and HPV18, with some exceptions (see below). In HPV16, we did not find a qualified siRNA for gene E5 based on the parameters we set for selection in silico. We found 7 qualified siRNAs for gene E4. Among the 55 siRNA molecules for HPV16, three of them (#231, #232 and #315) are with Potency Enhancer Motif (PEM) (GGAGU/ACUCC) sequences, and targeting genes L2 and L1, respectively (Table 1). #163 and #167 target both genes of E2 and E4. The overlap has reduced the total number of unique sequence of siRNA to 53.

In HPV18, there are 7 and 6 siRNAs qualified for genes E4 and E5, respectively, based on our selection criteria summarized in previous section (Table 2). In addition, #173 and #178 target both genes E2 and E4. Thus our total number of unique siRNAs for HPV18 is 59 (Table 2). Among the 59 siRNA molecules for HPV 18, 9 of them (#25, $26, #38, #78, #79, #87, #345, #350, and #351) are with Potency Enhancer Motif sequences. Two of the siRNA molecules (#25 and #26) are for E6 gene, one (#38) is for E7 gene, three (#78, #79, and #87) are for E1 gene, and three (#345, #350 and #351) are for L1 gene (Table 2).

Cloning of 8 Genes (E6, E7, E1, E2, E4, E5, L2, and L1) from HPV16, 18, 6 and 11 in Luciferase Expression Vector to Make Fusion Genes

HPV16, 18, 6 and 11 genes were cloned into psiCHECK1/2 vector (FIG. 2. produced by Promega, a dual luciferase system with build-in internal luciferase control system). XhoI and EcoRI restriction enzyme sites were added in the 5′ and 3′ and of PCR amplified genes, and fused to the luciferase gene in the same open reading frame (ORF). Each construct harbors one or more genes depending on the size of the genes. After cloning, the constructed plasmids were used to transfect HeLa cells and permanently integrate the genes into the chromosomes to get stable cell lines. As an alternative, each construct could also be used in transient transfection together with the siRNAs for testing of gene expression knocking down (silencing) by siRNA. After the establishment of the cell line, a time course of Renilla luciferase activity was titrated. Then the specific gene knock-down was evaluated by the luciferase expression level. If transient transfection system was used, then co-transfection or stepwise transfection was applied with siRNA designed for screening by luciferase assay with proper controls.

Screen siRNAs in Cell Lines Harboring HPV Genes

SiHa is a cervical carcinoma cell line harboring HPV16 genome and expressing oncoproteins E6 and E7 [25, 26]. SiHa cell line was used to screen the function of siRNAs targeting E6 and E7 genes in the strain of HPV16. SiHa cells was grown in RPMI 1640 medium supplemented with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 100 μM non-essential amino acids, 1 mM sodium pyruvate, 50 μM 2-ME, 400 μg/ml G418 and 10% NCTC-109 medium at 37° C. with 10% CO₂. The cells were transfected with siRNAs complexed with LipofectAmine 2000 according to manufacturer's instruction. The cells were harvested and qRT-PCR was applied to evaluate the gene expression level of E6 and E7. The same cell samples were applied for ELISA and Western analysis.

Similarly, HeLa cervical carcinoma cell which has HPV 18 genome integrated in the cellular genome [27] was used to screen siRNAs targeting HPV 18 genes' expression. The cells were grown in the medium similarly described in above section. The siRNA transfection, qRT-PCR, ELISA and Western were followed the same procedures.

For siRNAs targeting HPV6 and 11, the screen was applied HPV6b cDNA-based C33A (non-cervical carcinoma) cell line [28]. The cells were grown in the medium described above. The siRNA transfection, qRT-PCR, ELISA, and Western will follow the procedure described in the previous section.

Validation of siRNA Cocktail in Cell Line In Vitro Transfection of siRNA

SiHa cells, maintained in Dulbecco's Minimal Essential Medium (DMEM) containing 10% fetal calf serum (FCS) and 20 mM glutamine, were examined for the ability of individual siRNAs to knock down particular gene targets. Cells were transfected using a Lipofectamine 2000 (Invitrogen, CA). Briefly, the cells were seeded (1×105 per well) in a 6-well plate in 2 ml of DMEM medium. The siRNA was diluted in 0.2 ml serum-free Opti medium mixed with 3 μl of the transfection reagent, incubated for 30 min at room temperature, then added drop-wise into the cell culture. Target mRNA and protein levels and effects on cells were analyzed in 48 h.

Screening siRNAs Against HPV16, 18, 6 and 11 Genes in HeLa229 by Measuring Luciferase Strength

HeLa229 cell line (ATCC) has been co-transfected with the plasmids encoding the fusion gene of HPV viral gene and luciferase and each of correspondent siRNA. In the controls, the vector with only the luciferase, or the fusion gene co-transfected with un-related siRNAs were used. The luciferase strength is measured in all the samples to screen the most active siRNA molecules which can knock down the expression of luciferase. After luciferase assays, the same samples were applied for RT-PCR, ELISA and Western analysis. After screening analysis, two siRNAs for each gene in HPV16, 18, 6 and 11 will be selected for the combination and in vivo studies (below).

Screen siRNAs in Cell Lines Harboring HPV Genes

SiHa is a cervical carcinoma cell line harboring HPV16 genome and expressing oncoproteins E6 and E7 [25, 26]. SiHa cells were used to screen the function of siRNAs targeting E6 and E7 genes in the strain of HPV16. SiHa cells were grown in RPMI 1640 medium supplemented with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 100 μM non-essential amino acids, 1 mM sodium pyruvate, 50 μM 2-ME, 400 μg/ml G418 and 10% NCTC-109 medium at 37° C. with 10% CO₂. The cells were transfected with siRNAs complexed with LipofectAmine 2000 according to manufacturer's instruction. The cells were harvested and qRT-PCR was applied to evaluate the gene expression level of E6 and E7. The same cell samples were also applied for ELISA and Western analysis.

Similarly, HeLa cervical carcinoma cell, which has HPV 18 genome integrated in the cellular genome [27], was used to screen siRNAs targeting HPV 18 genes' expression. The cells were grown in the medium similarly described in above section. The siRNA transfection, qRT-PCR, ELISA and Western were followed the same procedures.

Gene Knock-Down Assay by RT-PCR Analysis

The gene knockdown results can be evaluated by measuring the mRNA changes within siRNA treated cells using RT-PCR to amplify RNA isolated from corresponding cells. Selection of the appropriate upstream and downstream primers is the initial step for evaluation of targeted gene knockdown and choice of the appropriate cell lines. The sequences of the primers for RT-PCR analysis are:

HPV16 PCR primer list HPV16-1: 16E6-1F (191-461): GGAATCCATATGCTGTATGT PCR length: 270 bp 16E6-1B (191-461): CTACGTGTTCTTGATGATCT HPV16-2: 16E6-2F (278-448): CAACATTAGAACAGCAATAC PCR length: 170 bp 16E6-2B (278-448): ATGATCTGCAACAAGACATA HPV16-E7-1: 16E7-1F (21-43): ATTGCATGAATATATGTTAGATT PCR length: 250 bp 16E7-1B (248-270): CACAATTCCTAGTGTGCCCATTA HPV18 PCR primer list HPV18-1: 18E6-1F (65-84): ACACTTCACTGCAAGACATA PCR length: 196 18E6-1B: (241-260): CCATACACAGAGTCTGAATA HPV18-2: 18E6-2F (107-126): AGACAGTATTGGAACTTACA PCR length: 151 18E6-2B (238-257): TACACAGAGTCTGAATAATG HPV18-E7-1: 18E7-1F (38-54): TGCATTTAGAGCCCCAA PCR length: 253 18E7-1B (275-291): CACAAAGGACAGGGTGT

Total RNA was extracted from cell culture or tumor tissues with RNeasy mini kit (Qiagen, Valencia, Calif.) according to the manufacturer's instructions. For RT-PCR, the first cDNA strands were synthesized by using cDNA Synthesis Kit (GE Healthcare, Chicago, Ill.) according to the manufacturer's instructions. The PCR reaction was started with lower cycle numbers, from 25, 30 to 35 to avoid the possible amplification plateau. Both Geneamp 9700 Thermalcycler and Taqman (ABI, CA) were used for PCR analysis. The amplicons were subjected to the gel electrophoresis analysis.

ELISA Assay for Luciferase Expression

The HPV gene expression after siRNA knock down could be evaluated by the protein level assay of Luciferase through Enzyme Linked Immunosorbent Assay (ELISA), since all the HPV gene were fused with luciferase gene. The same samples were applied for ELISA assays for Luciferase.

ELISA with specific antisera will be used for validation of siRNA-mediated down-regulation targeted proteins according to the manufacturer's instructions. Antibodies against Luciferase will be purchased from Promega.

Western Analysis for Luciferase Expression

The HPV gene expression after siRNA knocking down was evaluated by Western analysis against HPV16-E7. The same samples used in the above assays were applied to Western analysis to evaluate gene down regulation by each specific siRNA molecule. Antibodies against HPV16-E7 were purchased from Promega.

SiRNA Cocktail

The most potent siRNA to down regulate each gene in HPV will be grouped to evaluate the function to knock-down several genes' expression within each of species of HPV16, 18, 6 and 11. Following that, a complex to include siRNAs targeting all 4 HPV species will be formed to get the final cocktail to target either early or late genes in HPV16, 18, 6 and 11.

SiRNA Duplex with Potency Enhancer Motif

The siRNA molecules with Potency Enhancer Motif (PEM) will be compared with other siRNA molecules in Luciferase assay, RT-PCR, ELISA and Western.

Selection of siRNAs with and without PEM Sequence

In our siRNA design, L2 and L1 from HPV16 have 2 and 1 siRNAs with PEM sequence, respectively. While in HPV18, E6, E7, E1, and L1 each have 2, 1, 3, and 3 siRNAs with PEM sequence (Table 1 and 2). Special attention will be paid to those genes and siRNAs. If the in vitro cell screening showed acceptable effectiveness of the siRNAs to inhibit designated gene inhibition, those siRNAs will be paired with the ones without PEM but target the same gene for further animal studies.

Validation of siRNA Cocktail Complexed with Dendrimer in a Rabbit Model

Dendrimer Selection

The anionic poly-(L-Lysine) dendrimer (PAMAM, the active ingredient of VivaGel®) was used to complex with selected siRNA duplexes. dendrimer alone or siRNA alone was compared with the complex of dendrimer and siRNAs at different ratios. Each designed group was applied in the cottontail rabbit model [24].

Complex of siRNAs with Dendrimer

Selected siRNA were formulated with dendrimer in the ratio found above. The testing condition in the animal included the dendrimer alone and siRNA alone as control. Non-relevant siRNA was also used as control.

Since the active ingredient of VivaGel® is an anionic poly-(L-Lysine), the ratio of siRNA with dendrimer was tested to reach the optimum surface charge of the complex so that the VivaGel® is still active as proved in other experiments. Non-relevant siRNA with similar charge was formulated with VivaGel® as control.

Therapeutic Program Verses Prophylactic Program

In the therapeutic program, the siRNA was applied on the animal skin after the virus was inoculated. While in the prophylactic program, siRNA was applied prior to the inoculation of the HPV virus. The time interval was tested to find the best time point to apply “prophylactic” siRNAs on the animals before the virus challenge.

Specifically, for example, if siRNA #231 and 232 (each with the PEM sequence) and #194 and 258 (both without PEM sequence) in HPV16 showed effectiveness in inhibiting HPV16 L2 gene expression in cell screening, the pair of #231 and 194, or the pair of #232 and 258, or the pair of #231 and 258, or the pair of #232 and 194 will be selected for further therapeutic and prophylactic studies. In both studies, each pair was applied on one rabbit. The siRNA with PEM (e.m. #231) and without PEM (e.m. #194) was applied on left and right side of the animal respectively, with increased dose (from 5 μg to 100 μg), and proper control. The virion particle was inoculated on the same spot prior to the siRNA for the treatment program, or after the application of siRNA for prophylactic program. The interval between two treatments was tested in a separate experiment to cover from 4 hours to 72 hours.

Chimeric HPV Virion Particle Preparation

Using pseudovirion technology, we produced infectious particles composed of a heterologous cottontail rabbit Papilloma virus (CRPV) genome encapsulated with HPV 16/18 or CRPV capsid proteins [29]. The CRPV genome contains the simian virus 40 (SV40) origin of replication (337 bp) cloned at the BglII site within the upstream regulatory region for improved CRPV genome amplification in the packaging cell line 293TT. Both homologous (CRPV capsid/CRPV genome) and chimeric (HPV 16 or 18 capsid/CRPV genome) Papilloma virion particles will be prepared according to the methods [29]. The virion particle prepared this way is infectious in vitro at low volume (<10 μl) to induce epidermal papilloma on New Zealand White rabbits [24].

Rabbit Skin Inoculation of HPV Virus and Treat with Complex of siRNA and Dendrimer

We used the established cottontail rabbit model [24] to test the efficacy of our siRNA and the complex of siRNA and dendrimer to inhibit the lesion formation on the animal skin (FIG. 3). Briefly, the siRNAs, dendrimer, and the formulated complex of siRNA and dendrimer were applied on three groups of six rabbit each in various amounts (5 μg to 100 μg), before or after the virus inoculation depending on the program used to test the efficacy. Four days after the final treatment, blood samples were collected for analysis of capsid-specific antibody by using an enzyme-linked immunosorbent assay (ELISA). Each serum sample was tested for the ability to bind CRPV, HPV16 and HPV18 L1-only virus-like particles (VLPs) adhered overnight on 96-well plates in PBS (pH 7.4) at 4° C.

Validation of siRNA Cocktail Complexed with HK Polymer in a Rabbit Model

HK Polymer Selection

H2K4b is a histidine-lysine polymer with MW of 11,137, and showed the highest activity to inhibit the growth of fugal strains, C. albicans and C. kefyr [18]. The structure of H2K4b is shown here:

KKK(KHKHHKHHKHHKHHKHHKHK)4 Because of its anti-fungus activity, H2K4b will be selected as the HK polymer to formulate with the designed siRNAs against HPV 16, 18, 6 and 11. Complex of siRNAs with HK Polymer

Selected siRNA were formulated with HK polymer in the ratio found as described above. The testing condition in the animal included the HK polymer alone and siRNA alone as a control. Non-relevant siRNA was also used as a control.

The ratio of siRNA with HK Polymer was tested to reach the optimum surface charge for efficient cell delivery. Non-relevant siRNA with similar charge was formulated with HK polymer as control.

Rabbit Skin Inoculation of HPV Virus and Treat with Complex of siRNA and HK Polymer

We used the established cottontail rabbit model [24] to test the efficacy of our siRNA and the complex of siRNA and HK polymer to inhibit the lesion formation on the animal skin (FIG. 3). Briefly, the siRNAs, HK polymer, and the formulated complex of siRNA and HK polymer were applied on three groups of six rabbit each in various amounts (5 μg to 100 μg), before or after the virus inoculation, depending on what program were used to test the efficacy. Four days after the final treatment, blood samples were collected for analysis of capsid-specific antibody by using an enzyme-linked immunosorbent assay (ELISA). Each serum sample was tested for the ability to bind CRPV, HPV16 and HPV18 L1-only virus-like particles (VLPs) adhered overnight on 96-well plates in PBS (pH 7.4) at 4° C.

Example 1 25 Mer siRNA is More Potent than 21 mer siRNA

Although initial studies mostly applied 19mer and 21mer siRNA duplexes, several lines of evidence showed that 23mer, 25mer and 27mer siRNA duplexes exhibited more potent silencing effects than 19mer and 21mer siRNAs did. We found that 25mer duplexes with blunt ends are the most potent inhibitors. We have tested a 25mer siRNA duplex targeting human VEGF gene, hVEGF-25c (sense: 5′-CACAACAAAUGUGAAUGCAGACCAA-3′; Antisense:5′-UUGGUCUGCAUUCACAUUUGUUGUG-3′), comparing it to a 21mer siRNA duplex, which has been tested many times as one of the most potent VEGF specific inhibitory duplexes, hVEGF-21a (sense: 5′-UCGAGACCCUGGUGGACAUTT-3′; antisense: 5′-AUGUCCACCAGGGUCUCGATT-3′), in the cell culture followed with Q-RT-PCR analysis (FIG. 4A). A similar study also was carried out with ELISA analysis for the difference between the 25 mer and 21 mer siRNA both targeting VEGF (FIG. 4B).

Example 2 Cell Lines and PCR Primers for Potent siRNA Screening

SiHa cells which host HPV16 genes was chosen as the in vitro cell model to screen siRNAs against E7 gene expression in both HPV16 and chimerical human rabbit papilloma virus. Transfected SiHa cells were also applied in Western to evaluate the E7 protein expression. HeLa cells which host HPV 18 genes was chosen as the in vitro cell model to screen siRNAs against E7 gene expression in HPV 18. Quantitative RT-PCR was used to evaluate the E7 gene expression for potent siRNA screening.

PCR primers used to monitor the E7 gene expression in SiHa cell line:

16E7-Forward: ATTGCATGAATATATGTTAGATT 16E7-Reverse: CACAATTCCTAGTGTGCCCATTA;

PCR primers used to monitor the E7 gene expression in HeLa cell line:

18E7-1Forward: TGCATTTAGAGCCCCAA 18E7-1Reverse: CACAAAGGACAGGGTGT.

Example 3 Design and Screen Small Interfering RNAs (siRNAs) Against E7 Gene in HPV16

The following are the DNA sequences in HPV16 E7 gene corresponding to each of the siRNA molecule. They all qualified in our in silica design system, and used as the model for siRNA syntheses.

Rec#, 34, GCATGGAGATACACCTACATTGCAT, Rec#, 37, GGACAGAGCCCATTACAATATTGTA, Rec#, 39, GCAAGTGTGACTCTACGCTTCGGTT, Rec#, 40, GCGTACAAAGCACACACGTAGACAT, Rec#, 41, CGTACAAAGCACACACGTAGACATT, Rec#, 42, GCACACACGTAGACATTCGTACTTT, Rec#, 43, GGAAGACCTGTTAATGGGCACACTA, Rec#, 44, CCTGTTAATGGGCACACTAGGAATT,

Through the in vitro SiHa cell screening, it showed that 4 out of 8 siRNAs reduced the E7 gene expression over 80% (FIG. 4).

Example 4 Construction of Chimerical Human Rabbit Papilloma Virus (cH-RPV)

Three epitopes (A, B and C in FIG. 5 top) from HPV16 E7 gene were applied to construct hybrid E7 gene between CRPV and HPV16. Epitope A corresponds to amino acid 82 to 90, while Epitope B corresponds to amino acid 49 to 57, and Epitope C corresponds to amino acid 11 to 20. The sequences were inserted at the end of CRPVE7 before the stop codon in the same open reading frame (ORF) to form a hybrid protein of E7 as shown (FIG. 5, bottom).

The potency of each of the hybrid viruses to form papilloma was confirmed in the rabbit skin.

Example 5 Design and Screen Small Interfering RNAs (siRNAs) Against E7 Gene in cH-RPV (Chimerical Human Rabbit Papilloma Virus)

CRPE7-36 5′- GCAUGAAUAUAUGUUGGAUCUGCA-3′ CRPE7-37 5′- GGACAGAGCCCACUACAACAUCGU-3′ CRPE7-38 5′- GCCCACUACAACAUCGUGACCUUUU-3′ CRPE7-43 5′- GGAAGACCUGCUGAUGGGCACCCU-3′ CRPE7-44 5′- CCUGCUGAUGGGCACCCUGGGCAU-3′ CRPE7-45 5′- GCACCCUGGGCAUCCUGUGCCCCAU-3′

Six siRNA shown above designed to target the three epitopes in the hybrid E7 gene, with CRPE7-36 targeting Epitope C, CRPE7-37 and CRPE7-38 targeting Epitope B, and CRPE7-43, -44 and -45 targeting Epitope A.

The results in FIG. 6 have shown that 4 of the hybrid siRNAs were able to reduce E7 gene expression over 60%, with #45 as the most potent siRNA which knocked-down E7 gene expression over 80%. The potency is listed as, 45 (0.197)>43 (0.305)>44 (0.350)>37 (0.383). The numbers in parentheses are the expression of E7 gene comparing with negative control.

Example 6 Design Small Interfering RNAs (siRNAs) Against E7 Gene in HPV18

The following are the siRNA sequences against corresponding sequences in HPV 18 E7 gene. They all qualified in our in silica design system.

HPV18E7-31: 5′- GCAUGGACCUAAGGCAACAUUGCAA-3′ HPV18E7-34: 5′- GGUUGACCUUCUAUGUCACGAGCAA-3′ HPV18E7-36: 5′- GCAAUUAAGCGACUCAGAGGAAGAA-3′ HPV18E7-38: 5′- CGAUGAAAUAGAUGGAGUUAAUCAU-3′ HPV18E7-39: 5′- CGAGCCGAACCACAACGUCACACAA-3′ HPV18E7-43: 5′- GCCAGAAUUGAGCUAGUAGUAGAAA-3′ HPV18E7-44: 5′- GCUCAGCAGACGACCUUCGAGCAUU-3′ HPV18E7-46: 5′- GCUGUUUCUGAACACCCUGUCCUUU-3′

Through the in vitro HeLa cell screening, it showed that 3 out of 8 siRNAs (#31, #36, and #38) are able to reduce the E7 gene expression over 50% (FIG. 7).

Example 7 Screen Small Interfering RNAs (siRNAs) Against E7 Gene in HPV18

FIG. 7 shows the effect of the designed siRNAs on knocking-down of HPV 18E7 mRNA expression. The transfections was done on HeLa cells, using 40 nM as the action concentration, and the 80 nM negative control siRNA as the NC group. β-actin was used as the internal control gene. Mean±SD.

The results demonstrated that three siRNAs (31#, 36#, 38#) showed fine knocking-down effect (>50%) targeting HPV16E7 mRNA expression. These three siRNAs were applied for the EC50 experiment.

Example 8 Western Analysis to Confirm the Knocking Down of E7 Protein Expression by Potent siRNAs

Four siRNAs against the hybrid E7 gene were further tested for their ability to reduce the E7 protein expression in SiHa cells by Western analysis. In FIG. 8, The Western blot (top) and quantitative data (bottom) showed that the potency of the siRNA reducing the E7 protein expression are listed in this order, −45>−43>−44>−37, which fit the results in the qRT-PCR.

Example 9 Testing the Efficacy of the siRNAs in Skin Infection Rabbit Animal Model (SIRAM)

CRPV/NZW rabbit in the testing In order to test the therapeutic efficacy of the siRNA we have confirmed with our in vitro cell screening system, 6 different wild type and hybrid viruses were inoculated on the NZW rabbit skin as illustrated in FIG. 9. Elizabeth collars (FIG. 9, right) were worn by each animal to avoid disturbing of the treated area by the animals.

In the pilot study six animals were used in the experiments. In each animal, L1-R1, L2-R2, L3-R3, L4-R4, L5-R5 and L6-R6 were challenged with six different constructs respectively as illustrated in the FIG. 7 legends. Two weeks after the challenge, the left sites of the papillomas were treated with corresponding testing siRNAs, N.C siRNA and Cidovofir topically for five consecutive days. Papilloma outgrowth began to be monitored at week 3 and until the termination of the experiment at the end of week 5. Pictures were also taken for record. Right sites are untreated control for the left treated sites. If the siRNA is effective, we should see smaller or no papillomas on the left sites but not on the right sites. The construct that infected L5-R5 sites is more vigorous than those on sites L2-R2, L3-R3 and L4-R4. L1-R1 infected with wild-type CRPV is used as a specificity control for the SiRNA. Therefore, if an epitope specific siRNA is effective, it should not influence L1-R1 sites but the sites that challenged with the constructs containing this epitope such as L5-R5.

The viruses are described in the following:

L1-R1, wt CRPV DNA 5 ug/site;

L2-R2, CRPV with HPV16E7/A 82-90 insert;

L3-R3, CRPV with HPV16E7/B 45-57 insert;

L4-R4, CRPV with HPV16E7/C 11-20 insert;

L5-R5, CRPV with HPV16 E7/82-90 at L2 insert;

L6-R6, CRPV tandem repeat with HPV16E7.

After papilloma appeared on the skin, we applied different siRNAs to the papilloma to evaluate the efficacy of them 2 weeks after the viral challenge. The following are the siRNAs applied on the animals:

Rabbit #3270, siRNA-CRPC-37;

Rabbit #3271, siRNA-CRPC-43;

Rabbit #3272, siRNA-CRPC-44;

Rabbit #3273, siRNA-CRPC-45;

Rabbit #3274, siRNA-NC;

Rabbit #3275, Cidofovir, the positive control;

In one of the examples, CRPV-43 treatment inhibited the papilloma growth (FIG. 10).

The ability of the siRNAs against the hybrid human rabbit papilloma growth was summarized in FIG. 11.

REFERENCES

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All publications, including issued patents and published patent applications, and all database entries identified by url addresses or accession numbers are incorporated herein by reference in their entirety.

Although this invention has been described in relation to certain embodiments thereof, and many details have been set forth for purposes of illustration, it will be apparent to those skilled in the art that the invention is susceptible to additional embodiments and that certain of the details described herein may be varied considerably without departing from the basic principles of the invention.

TABLE 1 HPV16 Sequences Corresponding to  the siRNAs Against 8 Genes (Potency Enhancer Motif, PEM,  is underlined and in bold font) HPV16 - 8siRNA Gene = “E6” (83 → 559)   #8, CCCACAGGAGCGACCCAGAAAGTTA  #10, CGACCCAGAAAGTTACCACAGTTAT  #11, CCACAGTTATGCACAGAGCTGCAAA  #15, CGACGTGAGGTATATGACTTTGCTT  #19, GGGAATCCATATGCTGTATGTGATA  #22, GCAATACAACAAACCGTTGTGTGAT  #28, CGGTGGACCGGTCGATGTATGTCTT  #30, CGATGTATGTCTTGTTGCAGATCAT Gene = “E7” (562 → 858)  #34, GCATGGAGATACACCTACATTGCAT  #37, GGACAGAGCCCATTACAATATTGTA  #39, GCAAGTGTGACTCTACGCTTCGGTT  #40, GCGTACAAAGCACACACGTAGACAT  #41, CGTACAAAGCACACACGTAGACATT  #42, GCACACACGTAGACATTCGTACTTT  #43, GGAAGACCTGTTAATGGGCACACTA  #44, CCTGTTAATGGGCACACTAGGAATT Gene = “E1” (865 → 2813)  #51, GGGTACGGGATGTAATGGATGGTTT  #64, CGGGTATGGCAATACTGAAGTGGAA  #81, GCTGCATTTGGACTTACACCCAGTA  #92, GGAGACACGCCAGAATGGATACAAA  #97, GGATTGTGCAACAATGTGTAGACAT #107, GGTGCAGCTAACACAGGTAAATCAT #118, GGATGTAAAGCATAGACCATTGGTA #130, CGATGGAGACTCTTTGCCAACGTTT Gene = “E2” (2755 → 3852) #131, GGAGACTCTTTGCCAACGTTTAAAT #135, GCTATTTATTACAAGGCCAGAGAAA #146, GGAAGTGCAGTTTGATGGAGACATA #151, GGGTCAAGTTGACTATTATGGTTTA #155, GGAAGTTCATGCGGGTGGTCAGGTA #163, CGACCCATACCAAAGCCGTCGCCTT #167, CCAAGATCAGAGCCAGACACCGGAA #172, GGCATTGGACAGGACATAATGTAAA Gene = “E4” (3332 → 3619) #158, GCAACGAAGTATCCTCTCCTGAAAT #159, CGAAGTATCCTCTCCTGAAATTATT #163, CGACCCATACCAAAGCCGTCGCCTT #164, GCCGTCGCCTTGGGCACCGAAGAAA #165, GGCACCGAAGAAACACAGACGACTA #166, GCACCGAAGAAACACAGACGACTAT #167, CCAAGATCAGAGCCAGACACCGGAA Gene = “E5” (3863 → 4099) No sequence can be qualified. Gene = “L2” (4235 → 5656) #192, CGTGCATCGGCTACCCAACTTTATA #202, GGGTACAGGCGGACGCACTGGGTAT #217, CCCAGATGTATCAGGATTTAGTATT #225, CGCCCAGTGGCACGCCTAGGATTAT #232, CC ACTCC CACTAAACTTATTACATA #247, GCAGCCTCACCTACTTCTATTAATA #259, CCAGGGTCTCCACAATATACAATTA Gene = “L1” (5559 → 7154) #265, GGCTGCCTAGTGAGGCCACTGTCTA #276, GCTGGTTTGGGCCTGTGTAGGTGTT #283, GCAGCAAATGCAGGTGTGGATAATA #289, CCCATGTACCAATGTTGCAGTAAAT #301, GGGTCTACTGCAAATTTAGCCAGTT #327, GGAGGCACACTAGAAGATACTTATA #345, CCTCATCTACCTCTACAACTGCTAA

TABLE 2 HPV18 Sequences Corresponding to the siRNAs Against 8 Genes (Potency Enhancer Motif, PEM, is underlined and in bold font) HPV18 - 8siRNA Gene = “E6” (105-581)   #6, GCAAGACATAGAAATAACCTGTGTA   #7, CCTGTGTATATTGCAAGACAGTATT  #12, CCCATGCTGCATGCCATAAATGTAT  #18, GGTGCCTGCGGTGCCAGAAACCGTT  #21, CCAGAAACCGTTGAATCCAGCAGAA  #24, GGGCACTATAGAGGCCAGTGCCATT  #25, CCGAGCACGACAGGAACG ACTCC AA  #26, GGAACG ACTCC AACGACGCAGAGAA Gene = “E7” (590-907)  #31, GCATGGACCTAAGGCAACATTGCAA  #34, GGTTGACCTTCTATGTCACGAGCAA  #36, GCAATTAAGCGACTCAGAGGAAGAA  #39, CGAGCCGAACCACAACGTCACACAA  #43, GCCAGAATTGAGCTAGTAGTAGAAA  #44, GCTCAGCAGACGACCTTCGAGCATT  #46, GCTGTTTCTGAACACCCTGTCCTTT Gene = “E1” (914-2887)  #50, GGGCACGGGTTGTAACGGCTGGTTT  #69, GGCAATGTATGTAGTGGCGGCAGTA  #78, GGGTTACAGCTATATTT GGAGT AAA  #79, GCTATATTT GGAGT AAACCCAACAA #104, CCTTATTAGCAGACAGCAACAGCAA #130, CGTGTTGGACATACTTTGATACCTA #142, GGAAGAGGAAGATGCAGACACCGAA Gene = “E2” (2817-3914) #144, CGAAGGAAACCCTTTCGGAACGTTT #151, GCAAGGGAACATGGCATACAGACAT #158, GGAATACAGAACCTACTCACTGCTT #163, GGACAGTGTGTATTATATGACTGAT #173, CGGTATCCGCTACTCAGCTTGTTAA #178, GCATTGTGGACCTGTCAACCCACTT #182, GGTAACACTACGCCTATAATACATT #187, GGAATACTGACTGTAACATACCATA Gene = “E4” (3418-3684) #172, CGACACGGTATCCGCTACTCAGCTT #173, CGGTATCCGCTACTCAGCTTGTTAA #174, GGTATCCGCTACTCAGCTTGTTAAA #175, CGCTACTCAGCTTGTTAAACAGCTA #178, GCATTGTGGACCTGTCAACCCACTT #179, CCACTTCTCGGTGCAGCTACACCTA #181, CGGAAACTCTGTAGTGGTAACACTA Gene = “E5” (3936-4157) #193, GCCATCTGTCTGTATGTGTGCGTAT #194, GCATGGGTATTGGTATTTGTGTATA #197, CCCTGCCACAGCATTCACAGTATAT #198, GCCACAGCATTCACAGTATATGTAT #199, CCACAGCATTCACAGTATATGTATT #201, GCCCATGTTACTATTGCATATACAT Gene = “L2” (4244-5632) #206, GCAAACGGGCTTCGGTAACTGACTT #221, GGGTACATTCCATTGGGTGGGCGTT #230, GGGTTTGATATAACATCTGCGGGTA #242, CCCTACATCTGGAACACATGGGTAT #253, CCTACCAACAAGTGTCAGTGGCTAA #262, GCAACTATGTTTACCCGCAGCGGTA #268, CGGAGGACAATGACTTGTTTGATAT #280, CCTCCTCTTGGGATGTGCCTGTATA Gene = “L1” (5430-7136) #288, CCTGCCTCTACACAGTATATTGGTA #307, GGGTGCAGTTACCTGACCCAAATAA #333, GGATATGGTGCCATGGACTTTAGTA #345, CCTCTG ACTCC CAGTTGTTTAATAA #350, GGTAGATACC ACTCC CAGTACCAAT #351, CC ACTCC CAGTACCAATTTAACAAT #364, CCAACTACTAGTTTGGTGGATACAT #379, CCACTACGTCTTCTAAACCTGCCAA

TABLE 3 HPV6 and HPV11 Common Sequences Corresponding to siRNAs (Potency Enhancer Motif, PEM, is underlined and in bold font) siRNAs common to HPV6 & 11 Gene = “E7” (530-826)  #3, CCTGTTGCTGTGGATGTGACAGCAA Gene = “E1” (832-2781)  #8, GGACAGTGGATATGGCTATTCTGAA #11, CGAGGAAGATGGAAGCAATAGCCAA #12, GGAAGCAATAGCCAAGCGTTTAGAT Gene = “E2” (2723-3826) #14, GGAAGTATGTTATGGCAGCACAGTT Gene = “L2” (4417-5784) #15, CCCTTTAGTCCTGTA ACTCC TGCTT #16, CCTTTAGTCCTGTA ACTCC TGCTTT #17, CCTGCTTTACCTACAGGCCCTGTTT Gene = “L1” (5771-7276) #21, GGCGGCCTAGCGACAGCACAGTATA #22, GCGGCCTAGCGACAGCACAGTATAT

TABLE 4 siRNAs against HPV16 E7 and hybrid CRPV E7 16E7-36: 5′ -GCAUGAAUAUAUGUUAGAUUUGCAA-3′ CRPE7-36: 5′ -GCAUGAAUAUAUGUUGGAUCUGCA-3′ 16E7-37: 5′ -GGACAGAGCCCAUUACAAUAUUGUA-3′ CRPE7-37: 5′ -GGACAGAGCCCACUACAACAUCGU-3′ 16E7-38: 5′ -GCCCAUUACAAUACCGUAACCUUUU-3′ CRPE7-38: 5′ -GCCCACUACAACAUCGUGACCUUUU-3′ 16E7-43: 5′ -GGAAGACCUGUUAAUGGGCACACUA-3′ CRPE7-43: 5′ -GGAAGACCUGCUGAUGGGCACCCU-3′ 16E7-44: 5′ -CCUGUUAAUGGGCACACUAGGAAUU-3′ CRPE7-44: 5′ -CCUGCUGAUGGGCACCCUGGGCAU-3′ 16E7-45: 5′ -GCACACUAGGAAUUGUGUGCCCCAU-3′ CRPE7-45: 5′ -GCACCCUGGGCAUCCUGUGCCCCAU-3′ 

What is claimed is:
 1. A composition comprising at least one siRNA molecule and a pharmaceutically acceptable carrier, wherein said siRNA molecule binds to an mRNA molecule that encodes at least part of a peptide or protein of a human papillomavirus (HPV).
 2. The composition of claim 1, wherein said siRNA molecule further comprises an immune stimulatory motif.
 3. The composition of claim 1, wherein said siRNA molecule comprises a potency enhancer motif.
 4. A composition comprising at least three siRNA molecules and a pharmaceutical carrier wherein the siRNA molecules bind at least three mRNA molecules that encode at least part of a peptide or protein of a HPV.
 5. The composition of claim 4, wherein said siRNA cocktail comprises three siRNA molecules at a ratio of 1:1:1, 1:1.5:0.5, or 0.5:0.5:2.
 6. The composition of claim 4, wherein the pharmaceutically acceptable carrier is selected from the group consisting of saline, sugar solutions, polypeptides, polymers, lipid, cream, gel, micelle materials, metal nanoparticles, dendrimers, and HK polymers.
 7. The composition of claim 6, wherein the carrier comprises a histidine-lysine copolymer that forms a nanoparticle with a siRNA molecule whose diameter is 100-400 nm.
 8. The composition of claim 6, wherein the carrier comprises a dendrimer.
 9. The composition of claim 6, wherein the carrier comprises a histidine-lysine polymer.
 10. A method for treating a mammal with an HPV infection comprising administering to said mammal a pharmaceutically effective amount of the composition of claim
 6. 11. A method for treating a mammal with an HPV infection and an HIV and/or an HSV infection comprising administering to said mammal a pharmaceutically effective amount of the composition of claim
 8. 12. A method for treating a mammal with an HPV infection and a fungal infection comprising administering to said subject a pharmaceutically effective amount of the composition of claim
 9. 13. The method of claim 10, wherein the mammal is a human.
 14. An isolated siRNA molecule that binds to an mRNA encoded by a gene in a HPV.
 15. A composition comprising at least three of the siRNA molecules of claim 14 and a pharmaceutically acceptable carrier.
 16. The composition of claim 15, wherein the pharmaceutically acceptable carrier comprises a dendrimer.
 17. The composition of claim 15, wherein the pharmaceutically acceptable carrier comprises a histidine-lysine polymer.
 18. The composition of claim 15, wherein said composition comprises at least three siRNA molecules at a ratio determined by the potency of each siRNA molecule and the therapeutic needs of the mammal.
 19. A method of treating a mammal with an HPV infection comprising administering to said mammal a pharmaceutically effective amount of the composition of claim
 15. 20. A method of treating a mammal with an HPV infection and with an HIV and/or HSV infection comprising administering to said mammal a pharmaceutically effective amount of the composition of claim
 16. 21. A method of treating a mammal with an HPV infection and with a fungal infection comprising administering to said mammal a pharmaceutically effective amount of the composition of claim
 17. 22. A nanoparticle comprising the siRNA molecule of claim 14, a pharmaceutically acceptable carrier, and a targeting ligand.
 23. A nanoparticle comprising three different siRNA molecules of claim 14, a pharmaceutically acceptable carrier, and a targeting ligand. 